The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

α-Amino-e-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5′-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and e-caprolactam-complexed form of ACLR at 2.21 and 2.40 A resolution, respectively. Based on the location of e-caprolactam in the complex structure, the substrate-binding site is assigned between Trp49 and Tyr137. The carboxyl group of Asp210 is a reasonable candidate that recognizes the nitrogen atom of a lactam or amide in the substrate. Based on a structural comparison with fold-type III alanine racemase, Tyr137 is potentially the acid/base catalytic residue that is essential for the two-base racemization mechanism. The overall structure of ACLR is similar to that of fold-type I enzymes. A structural comparison with these enzymes explains the different reaction specificities.